Documentation/Nightly/Modules/FinslerBacktracing

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For the stable Slicer documentation, visit the 4.6 page.


Introduction and Acknowledgements

Acknowledgments: Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware).

National Alliance for Medical Image Computing (NA-MIC)  


Module Description

The Backtracing Module uses the output of the Finsler Tractography Module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates.

Use Cases

Create fiber tracks from the output of Finsler Tractography Module

Tutorials

N/A

Similar Extensions

N/A

References

  • GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008

Information for Developers